You're right, I didn't specify a value for the hash, because it doesn't contain anything -- it's XS code acting like a hash, or in the problematic case, XS code acting like a scalar.

I tried the following which appeared to work in a trivial test case, but it corrupted memory causing a Segfault in another location when I tested it in real code:

my $aref = $f->getVariants(); # reference to array containing many Foo
my $sfoo = shift(@$aref);

my $tiefoo = {};

# warning - this causes segfaults
bless $tiefoo, 'Bar::Foo';
tie %{$tiefoo}, 'Bar::Foo', $sfoo;
$tiefoo->ACQUIRE();
[download]

So my conclusion is that it's not possible to fix this in pure Perl. The C++ or SWIG wrapper code must be modified.